Zap2It interviewed Craig Thomas and he talked a little bit about Barney/Robin - I definitely recommend the whole interview, which can be found
here, but the part you'll all be most interested in is this:
Now that you’ve seen Robarn together -- as in, in bed together -- how do you feel about the pairing? Is there more to come?
People will see in the finale that there’s definitely a hint of more to come. We love the two of them in teams together, we love the complication we’ve now added into their friendship. Most of the focus has been on patching up the relationship between Barney and Ted, but at some point we’re going to see that [Robin and Barney's] experience has [other] repercussions and is definitely going to mean something moving forward.